The school was founded in 1971 as a secular institution affiliated with St. Augustine By-the-Sea Episcopal Church in Santa Monica.

Crossroads started with three rooms in a Baptist church offering grades seven and eight, and an initial enrollment of just over 30 students.

[2]As St. Augustine's grew to junior and senior high school, the founders started Crossroads with a separate board of directors and separate campus, which eventually merged in the 1980s under the name Crossroads.

[3] The 2004 book Hollywood, Interrupted, by Andrew Breitbart and Mark Ebner, dedicated a large section to Crossroads; it depicted the school (and the celebrities who send their children there) in a negative light, focusing mainly on a handful of high-profile parents and "drug problems" stemming from the 1980s.

[1] Elon Musk alleges that Crossroads teaches “full-on communism,” and blames his daughter's transition, alleged communist ideology, and decision to cut him out of her life on Crossroads in his upcoming biography.